scPDB - 4y57 entry

Protein Data Bank Entry:

PDB ID : 4y57

Resolution :1.490 Å

Experimental Method : X-ray

Deposition Date : 2015-02-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endothiapepsin
ID:	CARP_CRYPA
AC:	P11838
Organism:	Cryphonectria parasitica
Reign:	Eukaryota
TaxID:	5116
EC Number:	3.4.23.22

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	11.280
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.882	695.250

% Hydrophobic	% Polar
41.75	58.25
According to VolSite

Ligand :

HET Code:	F63
Formula:	C11H13N2O2
Molecular weight:	205.233 g/mol
DrugBank ID:	-
Buried Surface Area:	57.51 %
Polar Surface area:	51.87 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
42.1547	2.67227	10.4721

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C5	CB	TYR- 79	4.07	0	Hydrophobic	false
C6	CB	ASP- 81	4.14	0	Hydrophobic	false
N14	OD2	ASP- 81	2.77	161.32	H-Bond (Ligand Donor)	false
N14	OD2	ASP- 81	2.77	0	Ionic (Ligand Cationic)	false
N14	OD1	ASP- 81	4	0	Ionic (Ligand Cationic)	false
N14	OG	SER- 115	2.77	149.03	H-Bond (Ligand Donor)	false
C4	CD2	LEU- 125	4.3	0	Hydrophobic	false
N2	O	HOH- 501	2.63	169.07	H-Bond (Ligand Donor)	false